We investigated prevalence and risk factors for methicillin-resistant Staphylococcus aureus (MRSA) in a case-control study performed in a 900-bed tertiary governmental healthcare facility in Bangkok, Thailand. Multivariate unconditional logistic regression was used to identify risk profiles for MRSA carriage. Phage typing, pulsed-field gel electrophoresis (PFGE), polymorphisms of the coa and spa genes, hypervariable region (HVR) of SCCmec, multi-locus sequence typing (MLST), and identification of ST30/ST8 mosaic chromosome by heteroduplex-polymerase chain reaction (heteroduplex-PCR) were used to demonstrate a clonal relationship. Fifty-seven of 619 in-patients (9.2%) were positive for MRSA. Risk factors were being male, long admission, low modified McCabe score, history of MRSA infection, and use of broad spectrum cephalosporin. Molecular typing results indicated close relatedness among MRSA isolates. Successful epidemic subtypes were recovered from many different wards. However, all subtypes with different multi-locus sequence types were single locus variants (SLVs) of ST239. Heteroduplex-PCR gave two positive bands from ST8/ST30 mosaic chromosomal structures in all SLVs indicating all isolates were of the ST239 origin. The burden of MRSA nosocomial infections is high in the governmental tertiary hospital. The sole ST239 and its SLVs identified in this hospital is striking and calls for better policy for infection control and prevention.